This seems fairly obvious, but I just discovered you can drag items from Stacks. So if you have something in your Downloads folder, for example, that you want to file, simply navigate to where you want to put the file, click on the Downloads stack in the dock, and drag the item you want to move from the stack to where you want it! This works with the spring-loaded dock and folders as well. Drag an image you just downloaded from the Downloads stack onto the iPhoto icon, wait for iPhoto to come to the front, then drag the photo into the album you want; you've just filed the photo without ever going to the Finder.

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